Captain Terry limped off after turning his ankle in the second half of the 0-0 first-leg draw in Madrid last Tuesday and Mourinho said then he was unlikely to play again this season.
Yet central defender Terry, who missed Sunday's 2-0 Premier League win at Liverpool, trained on Tuesday and has been decalred fit for the return at Stamford Bridge.
"He is ready and he will start," Mourinho said at his pre-match news conference on Tuesday.
Terry added that he was relishing the opportunity of playing after recovering from last week's knock.
"I'm fully fit, I've trained for three days and feel totally okay. Certainly walking off last week I didn't feel great at all and for two or three days in my head, I ruled myself out.
"But last Thursday it starting feeling better," he said.
Mourinho further backed his skipper, who is now 33, as being as good as he was when the Portuguese coach came to Chelsea in his first stint as manager a decade ago.
"He is at the same level now," said Mourinho, "and he deserves more from this competition than he has had. He lost the 2008 final in special circumstances and won the 2012 final in special circumstances so he deserves something more."
In 2008 Terry slipped and missed the penalty that would have given Chelsea victory in the penalty shootout in the final against Manchester United in Moscow which United won.
In 2012 he was suspended from the final against Bayern Munich but said he was now delighted to be on the cusp of playing in the club's third final.
"After the first one I wasn't sure we'd reach the final again and, after what has happened in the past, I am delighted we have another chance," he said.
Chelsea's Belgium playmaker Eden Hazard, who went off injured after 17 minutes of the quarter-final, second leg against Paris St Germain on April 8 and has not played since, is also available leaving Mourinho to decide if he will start.
But their Czech goalkeeper Petr Cech, who dislocated his shoulder last week, is not fit, although he trained on Tuesday.
"His condition does not give him a chance," Mourinho said.
Mourinho, whose defensive tactics frustrated free-scoring Atletico in Madrid, will also be without the suspended Frank Lampard and John Obi Mikel on Wednesday.
"A draw with a goal in it gives them the advantage," said Mourinho. "They are a very good team. They are not just a counter-attacking side they are a good side they defend well, they score a lot of goals and they win matches and they are in the semi-final of the Champions League and they need two victories to win the Spanish League title.
"For a team to do that against Barcelona and Real Madrid means they are a very good team."
Atletico manager Diego Simeone did not criticise Mourinho's defensive tactics last week, saying his opposite number did what he had to do to give his team an advantage for the second leg.
"I am a football man and I respect the different ways of how you can play the game," he told a news conference. "You have to congratulate a team that defends well.
"There is more than one way of playing football. If we all played the same way it would be very boring. You can play 10 at the back or one at the back - it is all the same, it is all about the result."
Simeone added it made little difference to him what team Atletico faced.
"They are a fantastic rival, a super-competitive opponent who are strong at the back and very good at set pieces. But we are confident. You don't get to the semi-finals of the Champions League and not feel confident."